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Function

Find and retrieve EMBOSS data files

Description

embossdata searches for a specified data file in all the directories which can hold them and writes the results of the search to screen or (optionally) to file. Optionally, all the files in the searched directories can be displayed. Optionally, it will also copy the file from the EMBOSS standard data directory to the current directory so that you can safely edit and use it.

Usage

Here is a sample session with embossdata

Display the directories searched for EMBOSS data files:

% embossdata
Find and retrieve EMBOSS data files
Data file name:
# The following directories can contain EMBOSS data files.
# They are searched in the following order until the file is found.
# If the directory does not exist, then this is noted below.
# '.' is the UNIX name for your current working directory.
. Exists
.embossdata Does not exist
/homes/user Exists
/homes/user/.embossdata Exists
/homes/user/local/share/EMBOSS/data/ Exists

Example 2

Display the names of data files in all of the possible data directories: This is run on a small test system and so the results will probably be different when you run this.

% embossdata EPAM60
Find and retrieve EMBOSS data files
# The following directories can contain EMBOSS data files.
# They are searched in the following order until the file is found.
# If the directory does not exist, then this is noted below.
# '.' is the UNIX name for your current working directory.
File ./EPAM60 Does not exist
File .embossdata/EPAM60 Does not exist
File /homes/user/EPAM60 Does not exist
File /homes/user/.embossdata/EPAM60 Does not exist
File /homes/user/local/share/EMBOSS/data/EPAM60 Exists

Command line arguments

Find and retrieve EMBOSS data files
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-filename] string This specifies the name of the file that
should be fetched into the current directory
or searched for in all of the directories
that EMBOSS programs search when looking for
a data file. The name of the file is not
altered when it is fetched. (Any string)
Additional (Optional) qualifiers (* if not always prompted):
-showall toggle Show all potential EMBOSS data files
* -fetch boolean Fetch a data file
-outfile outfile [stdout] This specifies the name of the file
that the results of a search for a file in
the various data directories is written to.
By default these results are written to the
screen (stdout).
Advanced (Unprompted) qualifiers:
-reject selection [3, 5, 6] This specifies the names of the
sub-directories of the EMBOSS data directory
that should be ignored when displaying data
directories.
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit

Qualifier

Type

Description

Allowed values

Default

Standard (Mandatory) qualifiers

[-filename](Parameter 1)

string

This specifies the name of the file that should be fetched into the current directory or searched for in all of the directories that EMBOSS programs search when looking for a data file. The name of the file is not altered when it is fetched.

Any string

Additional (Optional) qualifiers

-showall

toggle

Show all potential EMBOSS data files

Toggle value Yes/No

No

-fetch

boolean

Fetch a data file

Boolean value Yes/No

No

-outfile

outfile

This specifies the name of the file that the results of a search for a file in the various data directories is written to. By default these results are written to the screen (stdout).

Output file

stdout

Advanced (Unprompted) qualifiers

-reject

selection

This specifies the names of the sub-directories of the EMBOSS data directory that should be ignored when displaying data directories.

Choose from selection list of values

3, 5, 6

Associated qualifiers

"-outfile" associated outfile qualifiers

-odirectory

string

Output directory

Any string

General qualifiers

-auto

boolean

Turn off prompts

Boolean value Yes/No

N

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

N

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

N

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

N

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

N

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

Y

-help

boolean

Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose

Data files

No data files are read by this program.

Notes

Many EMBOSS programs use a data file. The data files are typically kept in a standard directory in the EMBOSS installation (.../emboss/emboss/data/). When an EMBOSS programs require a data file, it search for it in the following order of directories:

The current directory

.embossdata subdirectory in the current directory

Your home directory

.embossdata subdirectory in your home directory

The EMBOSS standard data directory

EMBOSS will use the data file it finds first from the above directories. For example, a data file in the current directory is used in preference to a file of the same name in the EMBOSS standard data directory.

It is sometimes necessary to modify a data file to change the behaviour of an EMBOSS program. To do this safely, you should copy the data file from the EMBOSS standard data directory to one of the other directories, such as the current directory or your home directory, before editing it. embossdata helps here by displaying the names of data files in all the directories which could hold them, and copying a data file from the EMBOSS standard data directory to the current directory.

By convention, all EMBOSS data file names start with the character 'E', to distinguish them from other files on your system. For example genetic codes to translate codons to amino acids are held in data files called "EGC.0", "EGC.1", "EGC.2", etc.

-filename option

Name of data file to search for or copy into the current directory from the EMBOSS standard data directory. The name of the file is not altered when it is fetched. (Any string is accepted).

-outfile option

Name of file containing the results of searching the data directories. By default this is written to the screen (stdout).

-reject option

The names of sub-directories of the EMBOSS data directory that should be ignored when displaying data directories.

References

None.

Warnings

None.

Diagnostic Error Messages

When copying a file, this program will report if the file has
been copied successfully, e.g.: